PDB entry 6vx4

View 6vx4 on RCSB PDB site
Description: Density-fitted Model Structure of Antibody Variable Domains of TyTx11 in Complex with Typhoid Toxin
Class: toxin
Keywords: Typhoid Toxin, A2B5, Antibody, Fab, TOXIN
Deposited on 2020-02-21, released 2021-02-24
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-07-14, with a file datestamp of 2021-07-09.
Experiment type: EM
Resolution: 3.12 Å
R-factor: N/A
AEROSPACI score: 0.16 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Pertussis like toxin subunit B
    Species: Salmonella enterica subsp. enterica serovar Typhi str. CT18 [TaxId:220341]
    Gene: pltB, D4F19_07865, D4F39_13740, D4G09_02615, D4X81_03235, D5848_06295, D5891_16360, D5B50_14740, D5C10_10475, D6331_06440, D6K86_15515, D6P24_09080, D6Q71_07195, D7N07_01470, D8R98_02600, D8S38_09485, DL104_04040, DLF44_02615, DM364_15630, DMA85_08120, DMV05_17400, DN022_06665, DN116_07470, DN223_02675, DNJ32_13915, DNL67_05455, DNM39_02515, DNV82_15785, DNV95_15160, DOH59_08615, DP757_14390, DPC06_03915, DPJ15_14935, DPS97_10830, DQ802_09840, DQD72_07750, DQJ57_09285, DRE79_02610, DRW87_14355, DRX58_02590, DRX79_07315, DS260_02735, DS269_05775, DS339_07525, DS529_00005, DSM93_00460, DST18_05335, DTV88_06700, DU090_09370, DUQ83_10880, DUW14_00135, DVF55_05015, EDK96_01785, EIT32_03595, EIT43_00570, YL55_10165
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Pertussis like toxin subunit B
    Species: Salmonella enterica subsp. enterica serovar Typhi str. CT18 [TaxId:220341]
    Gene: pltB, D4F19_07865, D4F39_13740, D4G09_02615, D4X81_03235, D5848_06295, D5891_16360, D5B50_14740, D5C10_10475, D6331_06440, D6K86_15515, D6P24_09080, D6Q71_07195, D7N07_01470, D8R98_02600, D8S38_09485, DL104_04040, DLF44_02615, DM364_15630, DMA85_08120, DMV05_17400, DN022_06665, DN116_07470, DN223_02675, DNJ32_13915, DNL67_05455, DNM39_02515, DNV82_15785, DNV95_15160, DOH59_08615, DP757_14390, DPC06_03915, DPJ15_14935, DPS97_10830, DQ802_09840, DQD72_07750, DQJ57_09285, DRE79_02610, DRW87_14355, DRX58_02590, DRX79_07315, DS260_02735, DS269_05775, DS339_07525, DS529_00005, DSM93_00460, DST18_05335, DTV88_06700, DU090_09370, DUQ83_10880, DUW14_00135, DVF55_05015, EDK96_01785, EIT32_03595, EIT43_00570, YL55_10165
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Pertussis like toxin subunit B
    Species: Salmonella enterica subsp. enterica serovar Typhi str. CT18 [TaxId:220341]
    Gene: pltB, D4F19_07865, D4F39_13740, D4G09_02615, D4X81_03235, D5848_06295, D5891_16360, D5B50_14740, D5C10_10475, D6331_06440, D6K86_15515, D6P24_09080, D6Q71_07195, D7N07_01470, D8R98_02600, D8S38_09485, DL104_04040, DLF44_02615, DM364_15630, DMA85_08120, DMV05_17400, DN022_06665, DN116_07470, DN223_02675, DNJ32_13915, DNL67_05455, DNM39_02515, DNV82_15785, DNV95_15160, DOH59_08615, DP757_14390, DPC06_03915, DPJ15_14935, DPS97_10830, DQ802_09840, DQD72_07750, DQJ57_09285, DRE79_02610, DRW87_14355, DRX58_02590, DRX79_07315, DS260_02735, DS269_05775, DS339_07525, DS529_00005, DSM93_00460, DST18_05335, DTV88_06700, DU090_09370, DUQ83_10880, DUW14_00135, DVF55_05015, EDK96_01785, EIT32_03595, EIT43_00570, YL55_10165
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Pertussis like toxin subunit B
    Species: Salmonella enterica subsp. enterica serovar Typhi str. CT18 [TaxId:220341]
    Gene: pltB, D4F19_07865, D4F39_13740, D4G09_02615, D4X81_03235, D5848_06295, D5891_16360, D5B50_14740, D5C10_10475, D6331_06440, D6K86_15515, D6P24_09080, D6Q71_07195, D7N07_01470, D8R98_02600, D8S38_09485, DL104_04040, DLF44_02615, DM364_15630, DMA85_08120, DMV05_17400, DN022_06665, DN116_07470, DN223_02675, DNJ32_13915, DNL67_05455, DNM39_02515, DNV82_15785, DNV95_15160, DOH59_08615, DP757_14390, DPC06_03915, DPJ15_14935, DPS97_10830, DQ802_09840, DQD72_07750, DQJ57_09285, DRE79_02610, DRW87_14355, DRX58_02590, DRX79_07315, DS260_02735, DS269_05775, DS339_07525, DS529_00005, DSM93_00460, DST18_05335, DTV88_06700, DU090_09370, DUQ83_10880, DUW14_00135, DVF55_05015, EDK96_01785, EIT32_03595, EIT43_00570, YL55_10165
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Pertussis like toxin subunit B
    Species: Salmonella enterica subsp. enterica serovar Typhi str. CT18 [TaxId:220341]
    Gene: pltB, D4F19_07865, D4F39_13740, D4G09_02615, D4X81_03235, D5848_06295, D5891_16360, D5B50_14740, D5C10_10475, D6331_06440, D6K86_15515, D6P24_09080, D6Q71_07195, D7N07_01470, D8R98_02600, D8S38_09485, DL104_04040, DLF44_02615, DM364_15630, DMA85_08120, DMV05_17400, DN022_06665, DN116_07470, DN223_02675, DNJ32_13915, DNL67_05455, DNM39_02515, DNV82_15785, DNV95_15160, DOH59_08615, DP757_14390, DPC06_03915, DPJ15_14935, DPS97_10830, DQ802_09840, DQD72_07750, DQJ57_09285, DRE79_02610, DRW87_14355, DRX58_02590, DRX79_07315, DS260_02735, DS269_05775, DS339_07525, DS529_00005, DSM93_00460, DST18_05335, DTV88_06700, DU090_09370, DUQ83_10880, DUW14_00135, DVF55_05015, EDK96_01785, EIT32_03595, EIT43_00570, YL55_10165
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: Cytolethal distending toxin subunit B
    Species: Salmonella enterica subsp. enterica serovar Typhi str. CT18 [TaxId:220341]
    Gene: cdtB, ABO08_07050, ACK79_04015, ACS18_04320, ADQ64_04510, AF726_04075, AG53_02460, AH360_09375, AH874_08650, AHN91_05150, AHS86_01310, AHX56_04670, AHY46_21185, AIA22_01750, AID13_25040, ALX58_21685, AU833_04405, AU920_00110, AXO05_06525, BXD49_09845, BXO48_02100, C3O10_15300, CIJ14_23185, D4382_23675, D4E01_03970, D4E24_23275, D4E82_03815, D4X65_01210, D4Y21_22955, D4Y61_01580, D5769_01120, D5773_04415, D5806_21735, D5905_00655, D5938_05180, D5A94_07255, D5B66_02920, D5P52_03820, D5W53_03345, D5X56_14350, D6J84_12220, D6Q32_04050, D6Q48_23450, D6Q50_22750, D6R14_01875, D6S47_01810, D6S52_04640, D7M89_03925, D7O59_01230, D8Q95_07260, D8R18_22625, D8R28_03780, D8R78_05465, D8S31_11805, D9P30_01530, D9P43_07260, D9Q66_22865, DAX91_01380, DJ817_22940, DJ902_22850, DK094_15420, DK681_22625, DK719_00065, DKA33_22680, DKS84_01205, DKT00_12650, DL111_03690, DLB36_01945, DLC21_01190, DM347_00605, DM358_02585, DMA89_03440, DML97_01185, DMM24_06680, DMU80_01195, DMU94_00450, DMV34_24005, DN115_03160, DN181_02750, DN218_09840, DN257_00960, DNM18_03225, DNP18_20975, DNU33_00605, DNU46_06990, DNV11_08545, DNV24_09060, DNV84_01240, DNZ24_19360, DNZ91_01190, DO736_07435, DO994_18310, DOA32_23160, DOC12_13865, DOC15_02915, DOC34_02235, DOG98_22220, DOH12_03665, DOQ73_02885, DOR42_02915, DOR52_05945, DOW79_02275, DOX21_23175, DP728_08755, DP748_00630, DP792_04070, DP807_22370, DP838_14200, DPC30_05570, DPD01_22830, DPD54_23140, DPE66_01635, DPE90_12380, DPJ07_11775, DPK35_02680, DPO73_22765, DPR96_19355, DPS68_01210, DPT88_22945, DPZ91_06800, DQ837_03030, DQ973_22635, DQ986_03355, DQC14_23020, DQC85_22655, DQJ66_20360, DQJ71_17745, DQK72_01185, DQR07_01185, DQS17_02890, DQS90_22855, DQY62_02055, DQZ13_01205, DRA30_01205, DRF26_01185, DRK15_02285, DRK71_19590, DRK91_13535, DRL63_05765, DRM75_04210, DRT15_23155, DRU74_02985, DRV60_04480, DRX43_08215, DRY73_10160, DRZ18_10315, DS251_02230, DS368_09485, DS470_09640, DS570_05080, DS689_07420, DSA82_02305, DSA99_17640, DSF62_00555, DSQ94_23515, DTE82_23795, DTF17_02235, DTF39_05055, DTG02_04520, DTG24_03875, DTG49_09625, DTG90_25155, DTH05_08145, DTT89_00540, DTU25_03425, DTW06_03295, DU078_23475, DU168_00610, DU852_01200, DU949_19355, DUA52_03235, DUC30_24990, DUE02_01595, DUP59_10365, DUQ37_03210, DUQ73_01530, DUR82_01195, DUR89_07585, DUU35_01075, DUU43_23100, DUU47_01595, DUV63_05900, DVF01_11150, EBC34_19090, EBC39_01055, ECA57_07075, ED432_03555, EDL32_22855, EGM22_03890, EGM32_22635, EHB26_00195, EHD17_22415, EHF16_02745, EIW64_10595, EIW71_22510, EIW76_01180, GX90_01205, JF03_03615, KO25_07020, LB54_02820, NCTC8272_01874, QC88_03775, R126_05570, R133_02035, RY52_03905, YR14_00925, ZG82_07355
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A447PE99 (0-246)
      • expression tag (247-254)
    Domains in SCOPe 2.08: d6vx4f_
  • Chain 'G':
    Compound: Pertussis toxin-like subunit ArtA
    Species: Salmonella enterica subsp. enterica serovar Typhi str. CT18 [TaxId:220341]
    Gene: artA, CIJ14_23170, D4382_23660, D4E24_23260, D4Y21_22940, D5806_21720, D6Q50_22735, D9Q66_22850, DJ817_22925, DJ902_22835, DKA33_22665, DOG98_22205, DP807_22355, DPD01_22815, DPO73_22750, DQ973_22620, DQC14_23005, DQC85_22640, DQS90_22840, EDL32_22840, EGM32_22620, EIW71_22495, PltA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6vx4g_
  • Chain 'H':
    Compound: Variable Domain of Heavy Chain of Antibody TyTx11
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VX4 (0-180)
  • Chain 'K':
    Compound: Variable Domain of Kappa Chain of TyTx11 Antibody
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VX4 (0-105)
    Domains in SCOPe 2.08: d6vx4k_

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >6vx4F (F:)
nisdykvmtwnlqgssasteskwnvnvrqllsgtagvdilmvqeagavptsavptgrhiq
pfgvgipideytwnlgttsrqdiryiyhsaidvgarrvnlaivsrqradnvyvlrpttva
srpvigiglgndvfltahalasggpdaaaivrvtinffrqpqmrhlswflagdfnrspdr
lendlmtehlervvavlapteptqigggildygvivdrapysqrvealrnpqlasdhypv
aflarsclehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6vx4F (F:)
nisdykvmtwnlqgssasteskwnvnvrqllsgtagvdilmvqeagavptsavptgrhiq
pfgvgipideytwnlgttsrqdiryiyhsaidvgarrvnlaivsrqradnvyvlrpttva
srpvigiglgndvfltahalasggpdaaaivrvtinffrqpqmrhlswflagdfnrspdr
lendlmtehlervvavlapteptqigggildygvivdrapysqrvealrnpqlasdhypv
aflarsc

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6vx4G (G:)
vdfvyrvdstppdvifrdgfsllgynrnfqqfisgrscsggssdsryiattssvnqtyai
arayysrstfkgnlyryqiradnnfysllpsityletqgghfnayektmmrlqreyvstl
silpeniqkavalvydsatglvkdgvstmnasylglsttsnpgvipflpepqtytqqrid
afgplisscfsigsvchshrgqradvynmsfydarpvielilsk

  • Chain 'H':
    No sequence available.

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6vx4K (K:)
diqmtqsssylsvsqgdrvtitckasdhidnwlawyqqkpgnaprllisgatslktglps
rfsgsgsgkdfslsitnlqtedvasyycqqywrtpytfgggtklei